maybe the new bolts are longer - how about some thin shims? or - a bit more drastic and difficult to get right - grind the nuts down a little. - i've gripped the nuts with a mole grip at an angle to undo / do up tricky crank bolts before - hard to get angle right but possible. you've greased this time due to past problems but it might not be the best idea to do it this time?
maybe the new bolts are longer - how about some thin shims? or - a bit more drastic and difficult to get right - grind the nuts down a little. - i've gripped the nuts with a mole grip at an angle to undo / do up tricky crank bolts before - hard to get angle right but possible. you've greased this time due to past problems but it might not be the best idea to do it this time?